/*
 * Help.hpp
 *
 *  Created on: May 16, 2012
 *      Author: marchi
 */

#ifndef HELP_HPP_
#define HELP_HPP_


const string Help=string("\n\n"
		"/------------------------------------------------------------------------------\\\n"
		"|                                                                               |\n"
		"| trjVoronoi computes the atomic Voronoi volumes and surfaces of a              |\n"
		"| molecular dynamic trajectory written in .dcd or .xtc format. It requires a    |\n"
		"| .pdb file containing the coordinates of the system, including waters          |\n"
		"| and ions. If the numbers of atoms in the .pdb and trajectory files            |\n"
		"| differ, the program *fails*.                                                  |\n"
		"|                                                                               |\n"
		"| The syntax of trjVoronoi is the following:                                    |\n"
		"|                                                                               |\n"
		"| trjVoronoi -help -b firstframe[0] -e lastframe[end] -dcd filein.dcd           |\n"
        "|             -xtc filein.xtc -o fileout -pdb filepdb -[no]rd -[no]hyd [nohyd]  |\n"
        "|             -[no]del [del]                                                    |\n"
        "|                                                                               |\n"
		"|                Default values in square backets []                            |\n"
		"|                                                                               |\n"
		"| *OPTIONS:                                                                     |\n"
		"|                                                                               |\n"
		"|        -help     Write this on line help                                      |\n"
		"|                                                                               |\n"
		"|        -b              First step to read from the trajectory                 |\n"
		"|                                                                               |\n"
		"|        -e              Last step to read from the trajectory                  |\n"
		"|                                                                               |\n"
        "|        -dcd            The trajectory file in .dcd format                     |\n"
		"|                                                                               |\n"
        "|        -xtc            The trajectory file in .xtc format                     |\n"
		"|                                                                               |\n"
		"|        -o              The binary output file                                 |\n"
		"|                                                                               |\n"
		"|        -pdb            The pdb file of the whole system                       |\n"
		"|                                                                               |\n"
        "|        -[no]rd         Do a radical Voronoi tesselation for polydisperse      |\n"
		"|                        system. The atomic radius is defined for the most      |\n"
		"|                        common elements found in a pdb file:                   |\n"
		"|                                                                               |\n"
		"|       double rd[]=  {0.3,1.75,1.65,1.55,1.76,1.2,2.02,1.05,1.2} Ang           |\n"
		"|       string elem[]={\"H\" ,\"C\"  ,\"N\"  ,\"O\"  ,\"S\"  ,\"NA\",\"CL\" ,\"MG\" ,\"CA\"};     |\n"
		"|                         The default value is -nord.                           |\n"
		"|                                                                               |\n"
		"|        -[no]hyd  Do the Voronoi calculation with[without] the system          |\n"
		"|                  hydrogens.  The default is *not* to include                  |\n"
		"|                  hydrogens.                                                   |\n"
		"|                                                                               |\n"
		"|        -[no]del  This option is of use only for parallel                      |\n"
		"|                  calculations. In this case each CPU operates on a            |\n"
		"|                  fraction of the trajectory and write the result to a         |\n"
		"|                  file on the local directory called ./.tmpfileXXXX            |\n"
		"|                  where XXXX is some random character string. At the           |\n"
		"|                  end of the run these results are appended to the             |\n"
		"|                  output file fileout. The option [no]del assure that          |\n"
		"|                  these scratch files are [not] deleted at the end of          |\n"
		"|                  the run. The default is to *delete* the files at the         |\n"
		"|                  end of the run.                                              |\n"
		"|                                                                               |\n"
		"|                                                                               |\n"
		"|      For more information contact Massimo.Marchi@cea.fr                       |\n"
		"|                                                                               |\n"
		"\\------------------------------------------------------------------------------/\n"
		);


#endif /* HELP_HPP_ */
